PhD Positions in Statistical Genomics/Computational Genomics

ETH Zürich Institute of Agricultural Sciences

Two PhD positions in Statistical Genomics / Computational Genomics

100%, Zurich, fixed-term

This is a unique opportunity for two doctoral students to participate in an international collaboration between two research institutes in Switzerland and Belgium. The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich and the Quantitative Genetics & Genomics group of Dr. Tom Druet from the University of Liège, Belgium, investigate DNA variation in individual animal genomes and at the population scale. Our groups apply state of the art technologies to sequence the genomes and transcriptomes of farm animals with long and short reads, and apply bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We offer two PhD positions at the interface of computational and statistical genomics, and bioinformatics.

Project background

The project «PangenomiX - Assessing impacts of sex chromosomal structural variants on reproduction- and meiosis-related traits in cattle through pangenomes and advanced imputation and association method» is a joint project co-developed by Dr. Tom Druet and Prof. Hubert Pausch. PangenomiX was recently funded as a Weave-project by the Fonds de la recherche scientifique (F.R.S.-FNRS) and the Swiss National Science Foundation.

PangenomiX aims to study how structural variants (SV) on the sex chromosomes contribute to genetic variation in complex traits, particularly those related to reproduction and meiosis. To this end, a new cattle pangenome that includes near complete assemblies of the sex chromosomes will be generated and statistical methods will be developed to transfer information from the pangenome variation panel to large mapping populations through imputation so that association testing between complex traits and SVs will eventually be possible.

This 4-years project builds upon previous research conducted by the Animal Genomics group and the Quantitative Genetics & Genomics group. We have collected large amounts of long read sequencing data (PacBio HiFi) to build genome assemblies and integrate them into pangenomes. This allowed us to investigate the distribution of structural variants in cattle and related species, construct different pangenome graphs, and identify trait-associated structural variants. Moreover, we have developed imputation methods that provide accurate genotypes in pedigreed populations, and haplotype-based association testing approaches, including some that had specifically been designed for the sex chromosomes.

PangenomiX will exploit large-scale long and short read sequencing data from two cattle populations to characterize structural variant diversity on the sex chromosomes, and investigate how these types of variants influence male fertility and recombiantion rates.

Job description

We are looking for two enthusiastic and highly-motivated candidates to work on the project.

• The first candidate will build pangenomes from long read sequencing data collected from two cattle breeds. Existing PacBio HiFi sequencing data will be complemented with ultra-long sequencing using ONT to build near complete assemblies for the sex chromosomes. This sub-project will be closely supervised by Prof. Hubert Pausch at ETH Zurich.
• The second candidate will focus on imputation and association testing. Approaches to impute structural variants into large mapping cohorts that had array- or short read sequencing-derived genotypes will be developed. The resulting genotypes will be tested for association with complex traits using methods that allow to account for the multi-allelic nature of the SVs. This sub-project will be closely supervised by Dr. Tom Druet at the University of Liége.

Close collaboration of both doctoral students is expected. Research exchanges between both groups are anticipated.

Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.

Profile

• Research interest in statistical genomics, computational biology, computational genomics, or animal genomics.
• Experience with a programming language (e.g., python, R) and basic working knowledge with high-performance computing clusters is required.
• A MSc degree in genetics, genomics, computational biology, bioinformatics, animal sciences or disciplines related to the PhD position.
• Affinity to computational genomics, bioinformatics or statistics is a pre-requisite.
• The writing of scientific papers and active participation in international conferences requires good knowledge of English.

Workplace

Zurich

We offer

An inspiring, supportive, and team-based research environment to facilitate seamless integration into an ambitious research project. Our team consists of a young and international group of researchers who share a common vision of contributing significantly to the highest-level academic research in the broad field of animal genomics. The team has an excellent track record of publishing in the field’s leading and key multidisciplinary journals. For a list of recent publications, see here.

Specifically, we offer

• integration into a young and dynamic research team with diverse backgrounds,
• own responsibility within a fully funded 4 year project,
• flexibility in designing and pursuing own research ideas within the scope of the overall project,
• collaboration with national and international partners,
• competitive salary conditions according to the regulations of the respective funding agency.

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We value diversity and sustainability

In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us – we are consistently working towards a climate-neutral future.

Curious? So are we.

Both projects are fixed term positions for 4 years with an anticipated start date of September 1st, 2026 (negotiable). Part of the data required to conduct the research have been collected, enabling also an earlier starting date of the project. You will either join the Animal Genomics group led by Hubert Pausch, or the Quantitative Genetics & Genomics group led by Dr. Tom Druet.

We look forward to receiving your online application with the following documents:

• Cover/motivation letter that demonstrates your suitability for the offered position and addresses the research questions you would like to develop within the doctoral project; please also indicate the sub-project you're most interested in,
• Curriculum vitae with complete academic record, copies of Bachelor and Master degrees,
• Name and contact information of two references.

Evaluation of applications will start April 7th, and continue until a suitable candidate has been identified. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.

Questions? Further information about the Animal Genomics group can be found on this website. Further information about the Quantitative Genetics group can be found on this website. For further information, please contact Prof. Hubert Pausch at e-mail hubert.pausch@usys.ethz.ch (no applications) or Dr. Tom Druet at e-mail Tom.Druet@uliege.be (no applications)

About ETH Zürich

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.